What is the best file format for configuration file?

Whatever. Comments are helpful, which makes pure JSON a poor choice. JSON5 or JSON-C are better, but linting and static analysis are important to every form of code, so make sure that what you use for that will understand your syntax.

My current preference is generally TOML, but I've started dabbling with custom HCL2 DSLs. (I write a lot of Go and Terraform.)